[English] 日本語
Yorodumi
- PDB-1cfe: P14A, NMR, 20 STRUCTURES -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1cfe
TitleP14A, NMR, 20 STRUCTURES
ComponentsPATHOGENESIS-RELATED PROTEIN P14APathogenesis-related protein
KeywordsPATHOGENESIS-RELATED PROTEIN / PR-1 PROTEINS / PLANT DEFENSE
Function / homology
Function and homology information


defense response to fungus / killing of cells of another organism / extracellular space
Similarity search - Function
CRISP family signature 2. / Allergen V5/Tpx-1-related, conserved site / CRISP family signature 1. / Cysteine-rich secretory protein-related / Pathogenesis-related Protein p14a / CAP / SCP / Tpx-1 / Ag5 / PR-1 / Sc7 family of extracellular domains. / CAP domain / CAP superfamily / Cysteine-rich secretory protein family ...CRISP family signature 2. / Allergen V5/Tpx-1-related, conserved site / CRISP family signature 1. / Cysteine-rich secretory protein-related / Pathogenesis-related Protein p14a / CAP / SCP / Tpx-1 / Ag5 / PR-1 / Sc7 family of extracellular domains. / CAP domain / CAP superfamily / Cysteine-rich secretory protein family / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Pathogenesis-related leaf protein 6
Similarity search - Component
Biological speciesSolanum lycopersicum (tomato)
MethodSOLUTION NMR / distance geometry
AuthorsFernandez, C. / Szyperski, T. / Bruyere, T. / Ramage, P. / Mosinger, E. / Wuthrich, K.
Citation
Journal: J.Mol.Biol. / Year: 1997
Title: NMR solution structure of the pathogenesis-related protein P14a.
Authors: Fernandez, C. / Szyperski, T. / Bruyere, T. / Ramage, P. / Mosinger, E. / Wuthrich, K.
#1: Journal: Plant Physiol. / Year: 1995
Title: Pathogenesis-Related Pr-1 Proteins are Antifungal. Isolation and Characterization of Three 14-Kilodalton Proteins of Tomato and of a Basic Pr-1 of Tobacco with Inhibitory Activity Against Phytophthora Infestans
Authors: Niderman, T. / Genetet, I. / Bruyere, T. / Gees, R. / Stintzi, A. / Legrand, M. / Fritig, B. / Mosinger, E.
#2: Journal: Embo J. / Year: 1985
Title: Amino Acid Sequence of the Pathogenesis-Related Leaf Protein P14 from Viroid-Infected Tomato Reveals a New Type of Structurally Unfamiliar Proteins
Authors: Lucas, J. / Camacho Henriquez, A. / Lottspeich, F. / Henschen, A. / Sanger, H.L.
History
DepositionNov 8, 1996Processing site: BNL
Revision 1.0Nov 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PATHOGENESIS-RELATED PROTEIN P14A


Theoretical massNumber of molelcules
Total (without water)14,9141
Polymers14,9141
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
Representative

-
Components

#1: Protein PATHOGENESIS-RELATED PROTEIN P14A / Pathogenesis-related protein / PATHOGENESIS-RELATED LEAF PROTEIN 6 / ETHYLENE INDUCED PROTEIN P1 / P14


Mass: 14914.463 Da / Num. of mol.: 1 / Fragment: RESIDUES 1 - 135
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Solanum lycopersicum (tomato) / Organ: LEAF / Production host: Escherichia coli (E. coli) / References: UniProt: P04284

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: SEE PAPER *JRNL*

-
Sample preparation

Sample conditionspH: 5.5 / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMXBrukerAMX6001
Varian UNITYPLUSVarianUNITYPLUS7502

-
Processing

NMR software
NameDeveloperClassification
OPALWUTHRICHrefinement
DIANAstructure solution
RefinementMethod: distance geometry / Software ordinal: 1
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more